error when running bbduk

1

Hi there,
I'm trying to run `bbduk` in order to remove adapters from my fastq files

    bbduk.sh in=R1_001.fastq.gz  out=clean_1.fastq.gz ktrim=r k=21 path=adapters.fa

But i've got this error:

/usr/bin/bbduk.sh: line 344: /usr/share/bbmap/calcmem: No such file or directory
/usr/bin/bbduk.sh: line 345: setEnvironment: command not found
/usr/bin/bbduk.sh: line 346: parseXmx: command not found
/usr/bin/bbduk.sh: line 350: freeRam: command not found
java -Xmxm -Xmsm -cp /usr/share/java/bbmap.jar jgi.BBDuk in=1_S1_L001_R1_001.fastq.gz out=clean_1_1.fastq.gz ktrim=r k=21 path=adapters.fa
Invalid maximum heap size: -Xmxm
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

PS:

java --version
openjdk 11.0.11 2021-04-20
OpenJDK Runtime Environment (build 11.0.11+9-Ubuntu-0ubuntu2.20.04)
OpenJDK 64-Bit Server VM (build 11.0.11+9-Ubuntu-0ubuntu2.20.04, mixed mode, sharing)

Any idea whats wrong?
Thank you!


bbduk


error

• 212 views

You need to make sure that the directory containing bbmap scripts is in your $PATH. So try

export PATH=$PATH:/path_to_dir_with_bbmap_scripts

and see if that fixes the problem. You can then amend your $PATH permanently via your .bashrc or profile file.


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